Worktree isolation

Contract

Field	Bound contract
Trigger	A new isolated worktree or branch is requested, an existing ref or PR needs isolation, feature work needs a gated workspace with setup and baseline tests (feature-gate mode), a run needs a manifest-tracked worktree (loop-run mode), or a candidate patch must be captured from an ephemeral worktree without touching the current checkout (capture-isolated-patch mode).
Authority	Reversible local: writes only the worktree directory, .worktrees/ or .loop-worktrees/ entries, a gitignore entry, symlinked hooks, manifest bookkeeping, or (capture-isolated-patch mode) a fresh temporary worktree and binary-safe patch under its parent temporary directory; rollback is removing the worktree and reverting those entries. Capture-isolated-patch mode never writes the original checkout. Loop-run mode never passes --force to git worktree remove. No remote mutation.
Side effect	Local write: creates or attaches an isolated git worktree and reports its exact path and status. Feature-gate mode also runs setup and the baseline test suite. Loop-run mode also maintains a status manifest under .loop-worktrees/. Capture-isolated-patch mode runs the command in an ephemeral worktree, captures stdout/stderr/exit code, and writes and returns a binary-safe patch file path or preserves the worktree on extraction failure.
Done	new-work and isolate-existing-ref modes have an isolated workspace the harness can see and manage, with no phantom state. feature-gate adds a green baseline suite or surfaces a failure. loop-run adds a manifest where every worktree has a legal status and no removal used --force. capture-isolated-patch writes and returns a binary-safe patch file path and command results, removes its temporary worktree after successful extraction, or preserves it and reports extraction failure; the original checkout is unchanged either way.

Inputs

1. Mode (required): one of new-work, isolate-existing-ref, feature-gate, loop-run, capture-isolated-patch. Default new-work when no ref is named and no gate, lifecycle, or patch capture is requested.
2. Ref to isolate (isolate-existing-ref only): a PR head, branch, or commit.
3. New branch name (optional): derived from the work description when omitted.
4. Base branch (optional): defaults to origin's default branch, else main.
5. Setup command (feature-gate, optional): project setup to run inside the worktree, for example pnpm install --frozen-lockfile. When omitted, no setup step runs.
6. runId (loop-run, required): unique run identifier used verbatim as a path segment and branch suffix; a single path segment (no /, not . or ..).
7. pattern (loop-run, required at create): short work-pattern label kept on the manifest entry for audit.
8. Status for mark (loop-run, required): exactly one of active, rejected, escalated, merged, stale.
9. Cleanup set (loop-run, optional): status CSV, default rejected,escalated, plus an optional age cutoff <n> + s|m|h|d (for example 24h).
10. Command (capture-isolated-patch, required): shell command that produces the candidate change; run it inside the ephemeral worktree with that worktree as its working directory.
11. Base ref (capture-isolated-patch, optional): git ref used to create the detached worktree; defaults to the current HEAD.
12. Repo path (capture-isolated-patch, optional): repository path for validation and worktree creation; defaults to the current working directory.

Procedure

1. Determine the mode from the inputs. For capture-isolated-patch, require command and resolve optional base-ref and repo-path; for other modes, do not create a worktree for single-task work that can happen on a branch in the current checkout. Done when: the mode is decided, capture inputs are resolved when applicable, and single-task work is ruled out for other modes.
2. Mode capture-isolated-patch: verify repo-path is a git work tree and base-ref resolves, both scoped to repo-path: git -C <repo-path> rev-parse --is-inside-work-tree and git -C <repo-path> rev-parse --verify <base-ref>. Stop and report the exact failing check before creating any worktree if either fails. For other modes, detect existing isolation before creating anything by comparing the resolved absolute git dir against the resolved absolute common git dir: run git rev-parse --absolute-git-dir and (cd "$(git rev-parse --git-common-dir)" && pwd -P). Equal paths are a normal checkout and continue to step 5; different paths continue to step 3 for the existing-isolation check. Done when: capture validation passes or its failing check is named, or the non-capture comparison establishes equal or different paths and routes accordingly.
3. Mode capture-isolated-patch: create an ephemeral worktree at a fresh temporary path with git -C <repo-path> worktree add --detach <tmp-path> <base-ref> and record <tmp-path>. Report the git error if creation fails. For other modes after a different-path result from step 2, run git rev-parse --show-superproject-working-tree. Non-empty output means a submodule: in feature-gate mode stop and report that isolation must run from the superproject; in other modes treat it as a normal checkout and continue to step 5. Empty output means the run is already in an isolated worktree: report the worktree path (git rev-parse --show-toplevel) and current branch. In new-work and feature-gate modes proceed in place and skip to the mode steps. In isolate-existing-ref mode check the named ref out here unless it is already the current branch, then stop. For non-capture modes, do not create another worktree. Done when: the capture worktree is created and recorded or its git error is reported, or non-capture isolation is handled and the normal-checkout path continues to step 5.
4. Mode capture-isolated-patch: run command inside the ephemeral worktree, capturing stdout, stderr, and exit code; do not commit, push, or merge. After it returns, run git -C <tmp-path> add -N ., then compute git -C <tmp-path> diff --binary <base-ref> and write that binary-safe diff to a patch file under the worktree's parent temporary directory. A non-zero command exit still extracts the patch. If extraction succeeds, remove the worktree with git -C <repo-path> worktree remove --force <tmp-path> and return the patch file path, exit code, and outputs; if extraction fails, preserve the worktree and return its path, exit code, and failure reason. The original checkout remains untouched. Stop after this mode branch. Done when: the patch file path and command results are returned, or extraction failure is preserved for inspection.
5. Prefer the harness's native worktree primitive (for example Claude Code's EnterWorktree, a /worktree command, or a --worktree flag). Use it and continue to the mode steps. A behind-the-back git worktree add creates phantom state the harness cannot see, navigate to, or clean up. Done when: a native tool created the worktree, or no native tool exists and the git fallback is the next step.
6. If no native tool exists and steps 2-3 found no existing isolation, fall back to manual git worktree creation following references/git-fallback.md. In feature-gate mode, if creation fails (disk full, path conflict, locked index), fall back to in-place work on the current branch and report the fallback reason. Done when: the worktree exists under .worktrees/ and the harness can see it via the tracked convention, or the feature-gate fallback is reported.
7. Mode feature-gate: after the worktree exists (or in place after a fallback), run these steps in order. a. Gitignore entry: if the worktree directory is not already matched by .gitignore, add an entry for it and commit the change; skip when already ignored. Done when: the worktree directory is ignored by git. b. Symlink hooks: locate the parent repository's hooks directory via git rev-parse --git-common-dir from the worktree and symlink the worktree's hooks directory to it so shared hooks apply; on failure (permission, cross-filesystem) report it and continue without hooks. Done when: hooks are linked or the failure is reported. c. Run setup: if a setup command was supplied, execute it inside the worktree (or in place after fallback); on non-zero exit surface the error and stop. Done when: setup exits zero or the error is surfaced. d. Gate on baseline tests: run the project's baseline test suite inside the worktree (or in place); on failure surface the failures and ask the user to proceed or investigate. Done when: the baseline suite is green, or failures are surfaced with a proceed-or-investigate question.
8. Mode loop-run: manage the run under .loop-worktrees/ with these steps. a. Bind the root: run git rev-parse --is-inside-work-tree; on failure stop without mutating. The manifest is .loop-worktrees/manifest.json shaped exactly {"version":1,"worktrees":[]}; the mutex is .loop-worktrees/.manifest.mutex. If the manifest exists in any other shape, stop; never rewrite an unvalidated manifest. Add .loop-worktrees/ to .gitignore so worktree contents never enter the index. Done when: the root is bound and the manifest shape is validated. b. Serialize manifest mutations with the mutex: before each read-modify-write, create the mutex with exclusive create; if it exists and its mtime is older than 30 seconds, remove it and retry; otherwise retry after a short backoff until a 30-second deadline, then fail naming the mutex path. Delete the mutex when the mutation ends, success or failure. Pure reads take no mutex. Done when: each mutation ran under the mutex and the mutex is released. c. Create: refuse a runId that is not a single path segment. Under the mutex, read the manifest: if an entry with the same id has status active, refuse and name its existing path. Otherwise run git worktree add -b loop/<runId> .loop-worktrees/<runId> <base>, which creates the branch and checks it out in one step. Replace any prior entry with the same id and append {"id":<runId>,"path":".loop-worktrees/<runId>","branch":"loop/<runId>","baseBranch":<base>,"pattern":<pattern>,"createdAt":<ISO-8601 UTC>,"status":"active"}. Write the manifest atomically: write a temp file in the same directory, then rename it over manifest.json. Done when: the worktree and branch exist and the manifest records them atomically. d. Mark: under the mutex, reject any status outside the five-value set; find the entry by id or fail naming the id; set its status; write the manifest atomically. Never delete entries to record outcomes; removal happens only in cleanup. Done when: the entry carries the new legal status. e. Cleanup: under the mutex, select entries whose status is in the requested set (default rejected and escalated; active is never selected, so mark a finished run terminal first) and, when a cutoff is given, whose createdAt is older than now minus the cutoff. For each selected entry run git worktree remove .loop-worktrees/<id> without --force; a git refusal, typically uncommitted or untracked files, is recorded as skipped with its reason and the entry stays in the manifest. Rewrite the manifest without the removed ids, atomically. Done when: every selected entry is removed or recorded as skipped with its reason. f. Reconcile: list git worktrees with git worktree list --porcelain and compare paths under .loop-worktrees/ against the manifest. Worktrees registered with git but missing from the manifest are orphans: report them, and remove one only on explicit instruction, still without --force. Drop manifest entries whose directory no longer exists with an atomic manifest write. Treat a missing path as absent, not an error, since rm -rf, a crash mid-cleanup, or a container wipe can leave git listing a prunable entry. Done when: manifest and disk agree, or every divergence is reported.
9. For non-capture modes, report the worktree's absolute path and current branch, and confirm the harness can see it (native tool) or that it lives under the tracked .worktrees/ or .loop-worktrees/ convention (git fallback). Done when: the path, branch, mode, and creation method are reported.

Failure and recovery

• Bad input (capture-isolated-patch: missing command, non-repo repo-path, or unresolvable base-ref): stop before creating any worktree, report the exact check, and leave the original checkout unchanged.
• Worktree creation failure (capture-isolated-patch): no worktree exists; report the git error; the original checkout remains unchanged.
• Command exits non-zero (capture-isolated-patch): still extract the patch from its changes and return the non-zero exit code with stdout/stderr; this is not a skill failure.
• Extraction failure (capture-isolated-patch): preserve the ephemeral worktree and return its path plus the failure reason; do not delete it.
• Rollback (capture-isolated-patch): the original checkout is never written. On success, cleanup is git -C <repo-path> worktree remove --force <tmp-path> because the command modified the worktree; on extraction failure retain it for inspection.
• Already in an isolated worktree (non-capture modes): do not create another. Report the existing path and proceed in place (new-work, feature-gate) or check out the named ref there (isolate-existing-ref).
• Ref already checked out elsewhere (non-capture modes): report the existing checkout path; never create a second worktree for the same branch. Let the caller work in place or create a detached worktree at the same commit.
• "Worktree already exists" (non-capture modes): switch to it (cd .worktrees/<branch>) or remove it (git worktree remove .worktrees/<branch>) before recreating.
• "Cannot remove worktree: it is the current worktree" (non-capture modes): cd out first, then remove.
• Sandbox or permission error on git worktree add (non-capture modes): report the failure and ask the user for a blocking decision (work in the current checkout vs stop). Work in the current checkout only on explicit confirmation. In feature-gate mode, fall back to in-place work on the current branch and report the fallback reason.
• Submodule detected in feature-gate mode: stop and report that isolation must run from the superproject.
• Hook symlink fails (feature-gate): continue without hooks and report the failure.
• Setup command exits non-zero (feature-gate): stop, surface the error output, and do not proceed to the test gate.
• Baseline tests fail (feature-gate): surface the failures and ask the user to proceed with the isolated workspace or investigate first.
• Not a git repository (loop-run): stop before any mutation.
• Manifest in an unexpected shape (loop-run): stop without rewriting; report the corrupt manifest as the blocked result.
• Mutex deadline of 30 seconds (loop-run): fail naming .loop-worktrees/.manifest.mutex; if no other process is running, a mutex older than 30 seconds is cleared by the stale rule on the next attempt.
• runId already active (loop-run): create refuses; reuse the existing worktree or pick a new id; never double-create.
• loop/<runId> branch already exists (loop-run): surface the git refusal, then use a new id or explicitly delete the leftover branch from a prior attempt with the same id.
• Unrecognized status (loop-run): mark refuses before touching the manifest.
• Manifest write fails after git worktree add succeeded (loop-run): roll back to the pre-call state with git worktree remove .loop-worktrees/<runId> then git branch -D loop/<runId> (the branch points at the base, so nothing unique is lost), then rethrow; if the worktree removal is refused, report the path as an orphan for reconciliation instead of forcing it.
• Cleanup removes nothing on a freshly marked entry (loop-run): the age cutoff is working; this is expected, not a silent failure.
• Non-converged: if isolation cannot be established and no fallback is confirmed, return the blocked result with the exact error and the paths inspected. Never claim the done predicate holds.

Loop-run partial-result rule: every manifest write is tmp-then-rename inside the mutex, so readers never see a torn file, and every loop-run worktree on disk is either registered or rolled back. Capture-isolated-patch returns or preserves its temporary worktree as specified in step 4. No step is skipped without a reported reason.

Output

• capture-isolated-patch: a binary-safe patch file path, command exit code, and captured stdout/stderr; on extraction failure, the preserved worktree path, command exit code, and failure reason; the original checkout is unchanged.
• new-work and isolate-existing-ref: the isolated worktree's absolute path, current branch, mode used, and creation method (native tool or git fallback); or the existing worktree path and branch if already isolated.
• feature-gate: the workspace path and branch plus confirmation that the baseline suite is green; on in-place fallback, the current directory, branch, fallback reason, and test status; on test failure, the failure summary with a proceed-or-investigate question.
• loop-run create: the registered entry's worktree path, branch, and base branch. Mark: the entry id and its new status. Cleanup: removed <path> (<status>) and skipped <path>: <git reason> lines with counts. Reconcile: orphan paths and dropped entry ids. Reads: manifest rows <status> <id> <branch> (<pattern>).
• Terminal classification: done only when the Done predicate for the active mode holds; otherwise blocked with the exact error and the paths inspected.